I usually spend a lot of time organizing and the such. I also like a nice looking environment. I would like to propose a type of icon grouping. You would have the auto-expanding transparent windows, or any color you like, that would hold icons like containers. The icons would be on the desktop but grouped together visually to help organize. It is no different than just placing the icons close together, you just have some sore of visual cue behind the group.
Maybe you could also make the container do things like shade or rotate to an iconified position. I know this sounds a lot like just having a folder and then placing the icons in there but I think that would be too heavy. Plus this would be much more visually appealing.